J3_5NDJ_007

3D structure

PDB id

5NDJ (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of aminoglycoside TC007 in complex with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA (soaking)

Experimental method

X-RAY DIFFRACTION

Resolution

3.15 Å

Loop

Sequence

UUUAAUUC*GAAGAACCUUACC*GGGCGA

Length

27 nucleotides

Bulged bases

5NDJ|1|13|A|1598, 5NDJ|1|13|G|1599, 5NDJ|1|13|A|1601

QA status

Valid loop

Sequence variability

If this chain is mapped to an Rfam alignment, the link below will give its sequence variability.

R3DSVS

Structural variability across Equivalence Class

The link below will give the loop's structural variability across the equivalence class for this chain.

R3DMCS EC

Structural variability across Rfam

If this chain is mapped to an Rfam alignment, the link below will give the loop's structural variability between chains mapped to the same Rfam family.

R3DMCS Rfam

J3_5NDJ_007 not in the Motif Atlas

Homologous match to J3_6CZR_062

Geometric discrepancy: 0.1225

The information below is about J3_6CZR_062

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_59791.1

Basepair signature

cWW-F-F-F-F-F-tSS-F-F-F-F-F-F-F-F-F-F-cWW-F-F-F

Number of instances in this motif group

1

Unit IDs

5NDJ|1|13|U|1578
5NDJ|1|13|U|1579
5NDJ|1|13|U|1580
5NDJ|1|13|A|1581
5NDJ|1|13|A|1582
5NDJ|1|13|U|1583
5NDJ|1|13|U|1584
5NDJ|1|13|C|1585
*
5NDJ|1|13|G|1596
5NDJ|1|13|A|1597
5NDJ|1|13|A|1598
5NDJ|1|13|G|1599
5NDJ|1|13|A|1600
5NDJ|1|13|A|1601
5NDJ|1|13|C|1602
5NDJ|1|13|C|1603
5NDJ|1|13|U|1604
5NDJ|1|13|U|1605
5NDJ|1|13|A|1606
5NDJ|1|13|C|1607
5NDJ|1|13|C|1608
*
5NDJ|1|13|G|1847
5NDJ|1|13|G|1848
5NDJ|1|13|G|1849
5NDJ|1|13|C|1850
5NDJ|1|13|G|1851
5NDJ|1|13|A|1852

Current chains

Chain 13

16S ribosomal RNA

Nearby chains

Chain 1I

30S ribosomal protein S10

Chain 4I

30S ribosomal protein S13

Chain 5I

30S ribosomal protein S14 type Z

Chain AI

30S ribosomal protein S19

Chain W1

Transfer RNA; tRNA